I don't think it matters much because I presume the methane is extracted from both the biogas and the natural gas before it is fed into the reactor. what happens to the the CO2 and other trace gases from the biogas is that which is in the system already. The waste gases if natural gas is used should not be returned to the atmosphere because it would be increasing greenhouse gas load. In the case of my systems all of the biogas was burned either in a stove or an ICE running a pump.
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